That's an easy one: they should stay separated, they have very different concerns. In fact the BookingService should take a dependency on IBookingRepository .
The service manages the use case of a booking. Your controller just sends some input data tot the service, which process it (verify business rules, loads/update entities etc) then sends the new/updated entities to the repository.
Booking Service cares about business rules, Repository cares about persisting entities. Your repository should not contain any business rules, only persistence related details. At least when updating models. For querying, it's easier to use directly a query handler or a query repository/service (call it what you want).